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- PDB-5lb8: Crystal structure of human RECQL5 helicase APO form. -

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Basic information

Entry
Database: PDB / ID: 5lb8
TitleCrystal structure of human RECQL5 helicase APO form.
ComponentsATP-dependent DNA helicase Q5
KeywordsHYDROLASE / Helicase / RecQ / Transcription / DNA repair / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / DNA 3'-5' helicase / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA metabolic process / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / DNA 3'-5' helicase / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA metabolic process / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / helicase activity / replication fork / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / chromosome / mitotic cell cycle / DNA replication / nucleic acid binding / cell division / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNewman, J.A. / Aitkenhead, H. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5.
Authors: Newman, J.A. / Aitkenhead, H. / Savitsky, P. / Gileadi, O.
History
DepositionJun 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3May 3, 2017Group: Database references
Revision 1.4Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q5
D: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,7254
Polymers115,5942
Non-polymers1312
Water0
1
A: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8632
Polymers57,7971
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: ATP-dependent DNA helicase Q5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8632
Polymers57,7971
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.740, 68.740, 396.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ATP-dependent DNA helicase Q5 / DNA helicase / RecQ-like type 5 / RecQ5 / RecQ protein-like 5


Mass: 57797.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94762, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 17.5% Peg 3350, 0.2M Potassium Thiocyanate, 0.1M Hepes pH 7.0, 10% ethelene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.4→48.61 Å / Num. obs: 14135 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 120 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.7
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.61 Å / Cor.coef. Fo:Fc: 0.9164 / Cor.coef. Fo:Fc free: 0.8869 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.753
RfactorNum. reflection% reflectionSelection details
Rfree0.3218 684 4.87 %RANDOM
Rwork0.3014 ---
obs0.3025 14056 99.79 %-
Displacement parametersBiso mean: 145.41 Å2
Baniso -1Baniso -2Baniso -3
1--3.7405 Å20 Å20 Å2
2---3.7405 Å20 Å2
3---7.481 Å2
Refine analyzeLuzzati coordinate error obs: 0.812 Å
Refinement stepCycle: 1 / Resolution: 3.4→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 2 0 6566
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086692HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19063HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2307SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes987HARMONIC5
X-RAY DIFFRACTIONt_it6692HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.89
X-RAY DIFFRACTIONt_other_torsion21.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion880SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7512SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.67 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3552 141 5.06 %
Rwork0.3234 2644 -
all0.325 2785 -
obs--99.54 %

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